Abnormalities of the DNA Methylation Mark and Its Machinery
Abnormalities of the DNA Methylation Mark and Its Machinery
The effects of DNA cytosine methylation on gene transcription are performed in multiple ways. GC-rich motifs can act as binding sites for transcription factors, and CpG methylation can prevent binding of these factors, which can lead to repression of transcription. Additionally, gene expression can be modulated through the action of proteins that specifically bind to methylated DNA. These "readers" of the DNA methylation signal are known as methyl-CpG-binding proteins. These proteins are classified by the type of domains they contain that bind methyl-CpG. For example, the zinc finger protein family preferentially binds to methylated CpGs contained in a specific target sequence, and these proteins are thought to repress gene expression through their subsequent interaction with histone deacetylases. One zinc finger protein, ZBTB24, has been found to be a cause of ICF syndrome—ICF type 2 (Table 2), which shares most of the phenotypic characteristics of ICF syndrome resulting from DNMT3B mutations. ZBTB24 does not appear to directly bind methylated DNA, but is thought to modify transcription of genes through participation in epigenetic modifier complexes, thus producing a similar phenotype to ICF type 1.
Certain methyl-CpG binding proteins contain a specific methyl-CpG binding domain and are known as MBDs. The proteins in this family are MBD1–6 and methyl-CpG-binding protein 2 (MeCP2). Most of these bind to methyl-CpG (Fig. 1), with the exception of MBD3, MBD5, and MBD6. MBD1, MBD2, MBD4, and MeCP2 are thought to, among other functions, attract several other proteins to form chromatin remodeling corepressor complexes, which can repress gene expression at the corresponding loci. MBD5 and MBD6 are expressed in human brain and associate with heterochromatin, but do not bind to methylated DNA (Fig. 1). MBD5 is located at 2q23.1, and partial or complete deletions of this gene are associated with specific dysmorphic features, intellectual disability with language and speech particularly affected, seizures, and autistic features. These patients also demonstrate sleep disturbances, short stature, and brachycephaly. In vitro studies show that when MBD5 is deleted, there is a change in expression of RAI1 (implicated in Smith-Magenis pathophysiology), NR1D2 (a gene important for circadian rhythms), and MBD1. Some of the changes in expression of these putative target genes may therefore explain some of the subphenotypes of this disease. Patients with nonsense mutations or intragenic rearrangements of MBD5 have a very similar phenotype to those with a deletion. Interestingly, patients who have duplications in the region containing MBD5 have very similar neurodevelopmental phenotypes to patients with deletions, although on average less severe. The similarities between phenotypes in MBD5 deletion and duplication syndromes highlight the idea that concentrations of readers of DNA methylation, like most other components of the epigenetic machinery, are tightly controlled. Thus the associated neurologic phenotypes demonstrate a dose dependence, such that a disruption in either direction can cause disease. In fact, this dosage sensitivity appears to be a general feature of the Mendelian disorders of the epigenetic machinery.
Methyl-CpG-binding protein 2 (MeCP2) is the methyl-binding protein that has been studied most extensively. Although MeCP2 does have activity as a transcriptional repressor, extensive research has shown that it can also act as an activator depending on the other proteins to which MeCP2 binds while remaining bound to methylated CpGs (Fig. 1).
Deficiency of MeCP2 causes Rett syndrome–a neurodevelopmental disorder characterized by acquired microcephaly, progressive intellectual disability, loss of motor skills, and epilepsy. Rett syndrome occurs in 1 out of every 10,000 to 20,000 live births. Children with Rett syndrome have normal growth, head size and development until approximately 5 to 6 months of age when they demonstrate developmental stagnation and then regression, acquired microcephaly, and seizures. The majority (90%) of classical Rett syndrome cases are caused by loss of function mutations in MeCP2, located at Xq28. Those with classical Rett syndrome are generally girls who are heterozygous for the loss of function mutation. When boys with a MeCP2 mutation or deletion survive until birth, they exhibit a severe infantile encephalopathy with seizures. Rare cases of males with more classical Rett syndrome have been reported, and these cases either show significant somatic mosaicism or a 47XXY karyotype. Recently, Xq28 duplication (including MeCP2) has been found to be associated with a phenotype similar to classical Rett. Additionally, Rett syndrome severity correlates with the type of MeCP2 mutation, indicating that presence of a partially functional protein can ameliorate the disease phenotype.
MeCP2 is expressed in many tissues, but shows the greatest preference for mature neurons. When Mecp2 is knocked out either systemically or exclusively in neurons, the mouse Rett phenotype is present. Neurons in humans with Rett syndrome, neurons in Mecp2 knockout mice, and neurons derived from human stem cells with absent function of MeCP2 show reduced size of the cellular soma with decreased dendritic spine density and dendritic arborization. These abnormal cells have genome-wide downregulation of gene expression coupled with downregulation of protein synthesis, including some crucial for neuronal maturation and synaptic plasticity. Girls with Rett syndrome as well as Mecp2 knockout mice show significantly impaired synaptic function. Autopsy specimens of girls with Rett syndrome show increased NMDA receptor density at early ages, but decreased density thereafter in specific areas of the brain, which could explain some of the temporal developmental variation seen in Rett syndrome. Interestingly, mouse neurons show similar synaptic structural abnormalities when Mecp2 is duplicated, which is consistent with the phenotypic similarities in humans with the two conditions. This re-emphasizes the importance of tight regulation and dose dependence of MeCP2 activity (and DNA methylation "writing," "erasing," and "reading" in general) in neurologic functioning.
Defective Reading of the DNA Methylation Mark
The effects of DNA cytosine methylation on gene transcription are performed in multiple ways. GC-rich motifs can act as binding sites for transcription factors, and CpG methylation can prevent binding of these factors, which can lead to repression of transcription. Additionally, gene expression can be modulated through the action of proteins that specifically bind to methylated DNA. These "readers" of the DNA methylation signal are known as methyl-CpG-binding proteins. These proteins are classified by the type of domains they contain that bind methyl-CpG. For example, the zinc finger protein family preferentially binds to methylated CpGs contained in a specific target sequence, and these proteins are thought to repress gene expression through their subsequent interaction with histone deacetylases. One zinc finger protein, ZBTB24, has been found to be a cause of ICF syndrome—ICF type 2 (Table 2), which shares most of the phenotypic characteristics of ICF syndrome resulting from DNMT3B mutations. ZBTB24 does not appear to directly bind methylated DNA, but is thought to modify transcription of genes through participation in epigenetic modifier complexes, thus producing a similar phenotype to ICF type 1.
Certain methyl-CpG binding proteins contain a specific methyl-CpG binding domain and are known as MBDs. The proteins in this family are MBD1–6 and methyl-CpG-binding protein 2 (MeCP2). Most of these bind to methyl-CpG (Fig. 1), with the exception of MBD3, MBD5, and MBD6. MBD1, MBD2, MBD4, and MeCP2 are thought to, among other functions, attract several other proteins to form chromatin remodeling corepressor complexes, which can repress gene expression at the corresponding loci. MBD5 and MBD6 are expressed in human brain and associate with heterochromatin, but do not bind to methylated DNA (Fig. 1). MBD5 is located at 2q23.1, and partial or complete deletions of this gene are associated with specific dysmorphic features, intellectual disability with language and speech particularly affected, seizures, and autistic features. These patients also demonstrate sleep disturbances, short stature, and brachycephaly. In vitro studies show that when MBD5 is deleted, there is a change in expression of RAI1 (implicated in Smith-Magenis pathophysiology), NR1D2 (a gene important for circadian rhythms), and MBD1. Some of the changes in expression of these putative target genes may therefore explain some of the subphenotypes of this disease. Patients with nonsense mutations or intragenic rearrangements of MBD5 have a very similar phenotype to those with a deletion. Interestingly, patients who have duplications in the region containing MBD5 have very similar neurodevelopmental phenotypes to patients with deletions, although on average less severe. The similarities between phenotypes in MBD5 deletion and duplication syndromes highlight the idea that concentrations of readers of DNA methylation, like most other components of the epigenetic machinery, are tightly controlled. Thus the associated neurologic phenotypes demonstrate a dose dependence, such that a disruption in either direction can cause disease. In fact, this dosage sensitivity appears to be a general feature of the Mendelian disorders of the epigenetic machinery.
Methyl-CpG-binding protein 2 (MeCP2) is the methyl-binding protein that has been studied most extensively. Although MeCP2 does have activity as a transcriptional repressor, extensive research has shown that it can also act as an activator depending on the other proteins to which MeCP2 binds while remaining bound to methylated CpGs (Fig. 1).
Deficiency of MeCP2 causes Rett syndrome–a neurodevelopmental disorder characterized by acquired microcephaly, progressive intellectual disability, loss of motor skills, and epilepsy. Rett syndrome occurs in 1 out of every 10,000 to 20,000 live births. Children with Rett syndrome have normal growth, head size and development until approximately 5 to 6 months of age when they demonstrate developmental stagnation and then regression, acquired microcephaly, and seizures. The majority (90%) of classical Rett syndrome cases are caused by loss of function mutations in MeCP2, located at Xq28. Those with classical Rett syndrome are generally girls who are heterozygous for the loss of function mutation. When boys with a MeCP2 mutation or deletion survive until birth, they exhibit a severe infantile encephalopathy with seizures. Rare cases of males with more classical Rett syndrome have been reported, and these cases either show significant somatic mosaicism or a 47XXY karyotype. Recently, Xq28 duplication (including MeCP2) has been found to be associated with a phenotype similar to classical Rett. Additionally, Rett syndrome severity correlates with the type of MeCP2 mutation, indicating that presence of a partially functional protein can ameliorate the disease phenotype.
MeCP2 is expressed in many tissues, but shows the greatest preference for mature neurons. When Mecp2 is knocked out either systemically or exclusively in neurons, the mouse Rett phenotype is present. Neurons in humans with Rett syndrome, neurons in Mecp2 knockout mice, and neurons derived from human stem cells with absent function of MeCP2 show reduced size of the cellular soma with decreased dendritic spine density and dendritic arborization. These abnormal cells have genome-wide downregulation of gene expression coupled with downregulation of protein synthesis, including some crucial for neuronal maturation and synaptic plasticity. Girls with Rett syndrome as well as Mecp2 knockout mice show significantly impaired synaptic function. Autopsy specimens of girls with Rett syndrome show increased NMDA receptor density at early ages, but decreased density thereafter in specific areas of the brain, which could explain some of the temporal developmental variation seen in Rett syndrome. Interestingly, mouse neurons show similar synaptic structural abnormalities when Mecp2 is duplicated, which is consistent with the phenotypic similarities in humans with the two conditions. This re-emphasizes the importance of tight regulation and dose dependence of MeCP2 activity (and DNA methylation "writing," "erasing," and "reading" in general) in neurologic functioning.
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